The executable launcher, ZereneStacker, is written so that it can be accessed in any manner, including by symbolic link or being placed on the PATH. If you want to use a JRE other than the one provided with the distribution, just edit the zerenstk.ini template as desired.

The launch script ZereneStacker.bsh is written so that the package will run no matter where it is placed. You can launch it from the desktop or a file browser by double-clicking it and confirming either “Run” or “Run in Terminal”. Alternatively, you can execute it from a Terminal window as ZereneStacker/ZereneStacker.bsh (plus whatever path prefix is required to find the ZereneStacker directory).

For your convenience in using the package later, you may also want to create a “launcher” icon that will provide launch by double-click without the confirming dialog. The procedure for doing that depends on what version of Linux and what desktop manager you're using. Some helpful guidance is provided HERE at askubuntu.com.